I'm not sure exactly what you're asking, so if I haven't guessed right, please post back with some clarifying info...
If you and your spouse didn't live together at the end of the tax year (Dec 31st), you need to prepare your returns separately (i.e. they can't be prepared together at the same time).
You should still enter your marital status as married; TurboTax will then prompt you for the amounts you need from your spouse's return and visa-versa.
If you've already tried to prepare your returns together at the same time and find yourself stuck, here's how to start a new return: https://turbotax.community.intuit.ca/replies/3288128
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